Exam 3 Study Guide - PLPA 30003

What are typical viral symptoms

• Mosaic/mottle

• Yellowing (chlorosis)

• Stunting or reduced biomass

• Leaf deformation

What is the Central Dogma of Biology?

• DNA stores the biological information

• RNA delivers the information

• Proteins are the active information

How do viruses defy the central dogma of biology

• Viruses are non-cellular particles

• Have genomes

• Replicate

• Occupy a particular ecological niche

However they

• Lack a complete protein synthesis system

• Lack a complete energy generation system

Most plant virus genomes are?

Positive sense Single-stranded RNA

List the differences between a virus and a viroid

Viruses: Larger size, nucleic acid can be DNA or RNA, capsid surrounds genetic material, infects all types of organisms

Viroid: smaller size, nucleic acid is RNA only, no protein coat surrounds genetic material, only infects plants

Describe the role in the virus replication cycle of coat proteins

Make up the virion which protects the viral genome

Describe the role in the virus replication cycle of movement proteins

Allow the virus to move throughout the plant

Describe the role in the virus replication cycle of polymerase proteins

Allow the virus to replicate their genome

Describe the role in the virus replication cycle of silencing suppressor proteins

Allow virus to combat the defense system of the plant

What are the two types of virus movement within the host plant?

Cell-to-cell movement and long distance movement (through phloem)

Describe how cell-to-cell viral movement works

Travel through plasmodesmata (microscopic channels which traverse the cell walls of plant cells, enabling transport and communication between them). Viruses do not fit through the plasmodesmata so movement proteins are dedicated to enlarging the pore size of plasmodesmata and actively transporting the viral nucleic acid into the adjacent cell, thereby allowing local and systemic spread of viruses in plants

Describe how long-distance viral movement works

• Movement through the phloem

• Source to sink - leaves to roots

What are the viral mechanisms of long distance movement between plant hosts

• Sap (mechanical transmission, infected plant material - vegetative propagation, seed, pollen)

• Viruses are by carried vectors that create wounds

  • Insects, mites, nematodes, fungi and oomycetes, people (pruning or grafting)

How are plant viruses diagnosed?

• Bioassays - injecting sap from infected plant to indicator plant

• ELISA

• PCR (nucleic acid)

Describe how the Hawaiian papaya industry was saved from collapse

Transgenic UH rainbow and UH sunup varieties established in Puna that were bred for resistance of Papaya ringspot virus. Resistance was achieved by expressing RNA encoding coat protein. Introduction of virus genome into plant

What features makes for a successful vector?

• Ability to disperse

• Large host range

• High reproductive potential

  • Large populations

• Feeding behavior

  • Destructive vs delicate, tissue presence

• Piercing-sucking mouthparts (stylets)

• Hemiptera best vector group, aphids

Nonpersistent virus transmission

• Nonpersistent (stylet borne)

  • Acquisition time: short, seconds to minutes

  • Retention time: hours to days

  • No latent period

  • No multiplication in the vector

Persistent circulative virus transmission

• Acquisition time

  • Minutes to hours

• Retention time

  • Days to months

• Has a latent period

• Does not multiply in the vector

Persistent propagative

• Acquisition time 

  • Minutes to hours

• Retention time

  • Life of insect

• Has a latent period

• Does multiply in the vector

List management strategies for virus control and how they work 

• Resistant varieties, transgenic plants

• Use of certified virus-free seed or vegetative stocks

• Vector controls

  • Insecticides, stylet oils

• Cross protection

  • Inoculation with a mild strain to prevent infection with severe strains

• Seed treatment

  • Trisodium phosphate, virus contaminates seed coat

• Greenhouse

  • Wash tools with soap, 10% bleach or milk

• Quarantine

  • Prohibit entry of propagative material into the country or state

What is a nematode?

• Phylum = Nematoda (non- segmented round worms)

• Most numerous multicellular animals on Earth

Describe the life cycle of a plant parasitic nematode

Six stages: Egg, Four juvenile stages (J1, J2, J3, J4), adult

When does a plant parasitic nematode typically initiate parasitism of the plant?

J2

Describe the role of the stylet in plant parasitic nematodes?

• Specialized feeding structure

• Penetrate plant tissue

• Probe during feeding

• Secrete effectors and virulence factors

• Ingest plant cellular contents

What are ectoparasitic nematodes?

• Feed with probing stylet from the outside of plant tissue

• Mostly migratory

  • Move from cell to cell

  • May also move from plant to plant through the soil (vectors of plant viruses)

Examples of ectoparasitic nematodes

• Ring nematode (Criconemoides spp.)

• Xiphinema spp.

• Longidours spp.

What is an endoparasitic nematode?

• Enter plant tissue to feed from the inside

• Remain in the same part

• Some are migratory

  • Move through plant tissue, killing cells, cause massive plant tissue necrosis

• Some are sedentary

  • Induce the formation of specialized feeding sites and remain there until they die

Examples of endoparasitic nematodes

Meloidogyne sp. (Root knot), Heterodera sp. (Soybean cyst)

Describe the differences between migratory and sedentary nematode feeding strategies

• Migratory

  • Move through plant tissue, killing cells, cause massive plant tissue necrosis

• Sedentary

  • Induce the formation of specialized feeding sites and remain there until they die

What is a giant cell?

Enlarged cells, with nuclear division without cell division

Which nematode induces giant cell formations?

Root knot (Meloidogyne sp.)

How are nematodes diagnosed in a field setting?

• Presence of hot spots

• Stunting, wilting, yellowing

• Specific diagnosis requires analysis of soils and roots

What type of symptoms might you see above ground in nematode infestations?

Wilting, stunting, yellowing, presence of hot spots

What type of symptoms might you see below ground in nematode infestations

Galls, necrosis, cysts, stubby root system, forked roots, fibrous root proliferations

Describe foliar nematode disease

• Impact ornamental plants

  • Small spots between larger veins

  • V-shaped lesions along veins (veins limit movement)

  • Nematodes move from soil to leaves and enter through stomata

• White tip of rice

  • Aphelenchoides besseyi

  • Disseminates through seeds

  • Spikelets show chaffiness

  • Infestations can be limited by adequately irrigating the seedbed or direct sowing into water

Describe tree nematode disease

• Pinewood nematode (pine wilt disease)

  • Nematodes transmitted by beetles

  • Nematode blocks movement of water

    • Symptoms include wilting and yellowing of leaves

  • Can kill tree quickly

• Beech leaf disease

  • Litylenchus crenatae

  • Emerging threat to North American forest ecosystems

  • First discovered in Ohio (2012) and spreading

  • Live nematodes and nematode eggs can overwinter in beech leaf buds

  • Nematodes have been found in detached beech leaves on the ground after leaf fall in autumn

What are some disease complexes that include nematodes?

Fusarium-nematode wilt, Dagger nematode and cherry rasp leaf virus, tomato and tobacco ringspot virus

List the 3 most important plant parasitic nematodes

• Root-knot nematode - Meloidogyne

• Cyst nematode - Heterodera and Globodera

• Root lesion nematode - Pratylenchus

What are the key facts about Root-knot nematodes (symptoms, lifestyle, feeding habits)

• Meloidogyne spp.

  • Named for the galls or knots they induce

  • Sedentary endoparasites

  • Sexual dimorphism

    • Round, swollen adult females

  • Induce “giant cells” (permanent feeding sites)

    • Plant cell nucleus divides without cell division

    • Cell swells

  • Wide host range

  • Cause more crop losses than any other nematode

What are the key facts about cyst nematodes (symptoms, lifestyle, feeding habits)?

• Heterodera spp., Globodera spp.

  • Sedentary endoparasites

  • Create a syncytium (permanent feeding site)

    • Plant cell walls dissolve

  • Sexual dimorphism

    • Round, swollen adult females

    • Female protrudes from root

  • Host specific

What distinguishes the root lesion nematode from root knot nematode and cyst nematode

• They are migratory endoparasites

• No sexual dimorphism

  • All veniform (wormed-shaped)

What are nematode survival mechanisms?

• Crytobiosis/diapause

  • A reversible state of suspended metabolic activity during unfavorable conditions

• Cysts (Heterodera and Globodera)

  • Provide eggs with protection against dissection

• Eggs in soil

• Perennial plants

• Infected propagative plant parts

What management strategies can be used for the treatment of nematode infestation?

• Avoidance

  • Provide  adequate water and fertilizers to keep plants healthy

• Exclusion

  • Quarantines (local and international)

  • Plant pathogen-free propagative parts

• Eradication

  • Rotate to non-hosts

  • Remove weed hosts

  • Destroy infested plant debris

  • Use solarization

  • Steam soil

  • Apply nematicides

  • Biocontrol

• Protection

  • Plant resistant hosts

  • Natural metabolites

  • BT technology

What environmental factors should be considered when applying a nematicide?

Applying nematicides will eradicate beneficial nematodes. PPNs are only a small population of nematodes in the soil. Beneficial nematodes feed on bacteria, fungi, insects, and even harmful nematodes. Beneficial nematodes also contribute to soil health and are involved in nutrient systems

What type of genetic modification technology is being considered to combat nematode disease?

Bacillus thuringiensis - bacteria BT gene inserted into crop. When nematode feeds on cropit dies

What is the difference between an incubation period and a latent period?

Incubation period - time it takes from penetration to symptom appearance

Latent period - time it takes from penetration to production of secondary inoculum

Which is more critical when predicting an epidemic - incubation period or latent period?

Latent period

Lignin

Adds structural integrity to plant cell wall. Rigidity

Hemicellulose

Acts as glue of cellulose

Cellulose

Glucose cable that provides structure. Bulk of mass

What is the difference between passive and active defenses?

• Passive

  • Constitutive - always present.

• Active

  • Induced - activated by pathogen entry

Examples of passive structural defenses

Physical barriers

• Waxy cuticle

• Size and shape of stomata 

• Dense layer of hairs (trichomes)

• Suberized cells (tubers, bulbs)

• Lignification of woody tissues

• Collenchyma and sclerenchyma (protect vascular tissue)

Examples of passive chemical defenses

Always present

• Secondary metabolites - not needed for growth

  • Terpenoids (e.g. pyrethrins)

  • Phenolics, toxic compounds bound to sugars

  • Alkaloids, nitrogenous compounds (e.g. caffeine and nicotine)

  • Saponins - soapy

Examples of active structural defenses

• Activated by pathogen entry. Produced after infection

  • Leaf abscission

  • Tyloses

  • Cell wall reinforcement with lignin

  • Cell wall reinforcement with callose

  • Papillae

Examples of active chemical defenses

• Phytoalexins

  • Antimicrobial (toxic) agents

  • Low molecular weight

  • Plant specific, but broad-range activity

• Oxidative burst

  • Toxic to all cells (host and pathogen)

  • Destroy DNA

  • Oxidation of lipids and proteins

  • Can inactivate enzyme co-factors

• PR proteins - chitinases, etc

What does MAMPS stand for

Microbe Associated Molecular Patterns

Give examples of MAMPS

Cellular components of pathogen

• Chitin (fungal cell walls)

• Lipopolysaccharide (gram-negative bacteria cell wall)

• Flagellin

• Coat protein (virus)

What function do MAMPS have in the plant defense model

MAMPS are molecules that activate a plant’s first line of defense. Microbe triggered immunity, pathogenesis-related proteins are produced in response to pathogen attack. Chitinases that degrade chitin in fungal cell walls. Glucanases that degrade beta-glucans in fungal and bacterial cell walls. Proteases that degrade proteins

Draw the co-evolution model for plants and pathogens from Jones and Dangl (2006). Label PTI, ETS, and ETI on the model and define each

PTI

Pattern Triggered Immunity

ETS

Effector Triggered Susceptibility

ETI

Effector Triggered Immunity

Define pathogenicity genes

Genes that are essential for a pathogen to cause disease 

Define virulence genes

Genes that make a pathogen more devastating

How are effectors typically delivered by bacteria

By use of a syringe-like apparatus (Type III Secretion System)

How are effectors typically delivered by fungi

Haustoria

Hypersensitive response

Localized cellular sacrifice. Occurs after plant proteins (resistance proteins) recognize the presence of specific disease causing compounds (effector proteins) introduced into the the host by the pathogen

What is an effector

A protein produced by a pathogen that can regulate a biological activity in the host. Can sometimes act as avirulence proteins

What is systemic acquired resistance

The invasion of a pathogen in one location signals defense reactions in other parts of the plant

• The signal that is transported is associated with plant hormones

  • Salicylic acid (biotrophs)

  • Jasmonic acid (necrotrophs and herbivory)

  • Ethylene

• Elicits hypersensitive response

What is induced systemic resistiance

Induced by non-pathogens such as rhizobacteria. Pathogenesis-related (PR) proteins are not produced. Induces certain structural defenses and phytoalexins. These defenses are not always active because it requires a lot of energy

Define general (quantitative) resistance

Also known as: non-host resistance, horizontal resistance, polygenic resistance

• Most common, controlled by many genes, broad-spectrum plant defense, quantitative form of resistance

• Resistance to a single disease and is not effective against other diseases   

• Continuous variation among genotypes

• Many loci

Advantages and disadvantages of general (quantitative) resistance

Advantages: can control a broad range of races due to the fact that many loci are involved

Disadvantages: difficult to transfer resistance from one genotype to another. Individual genes harder to identify

Define specific (qualitative) resistance

Vertical resistance, monogenic (single-gene) resistance

• Controlled by a single gene

• Confers complete resistance against a specific race of the pathogen

• A qualitative form of resistance

• Distinct classes of resistant and susceptible plants

Advantages and disadvantages of specific (qualitative)resistance

Advantages: Easier screenings. Easier transfer of genes “all or nothing”

Disadvantages: vulnerability to new races. Continuous use of particular cultivar may lead to development of new race or shift in pest population (shift from race 1 to race 2)

Describe the boom and bust cycle of resistance breeding

1. New cultivar with R (resistant) gene is released

2. Cultivar attributes make it popular and it is widely planted

3. Selection pressure is placed on the pathogen to overcome the R gene

4. The cultivar is no longer disease-free

Explain how agrobacterium tumefaciens induces tumor formation in the wild

1. Attachment

2. Entry through wounds

3. Induction of T-DNA transfer - release of phenolics

4. Transformed cells divide rapidly - activation of bacterial genes

5. Tumor formation

Explain how scientists have co-opted Agrobacterium tumefaciens biology to create transgenic plants

1. Engineered (disarmed) TI-plasmid in agrobacterium

2. Co-cultured with explant tissues

3. Selection and regeneration of transgenic tissue/plants

TI -plasmid carrying desired genes, co-cultivation of agrobacterium with plant tissues, chromosomes with integrated DNA carrying desired genes, proliferation of transformed cells, shoot regeneration, regenerated plant with new trait

Insert our gene of interest into plant

Describe the gene gun method of plant transformation

Metal particles coated with DNA carrying desired genes, bombardment of plant tissues with DNA-coated particles (brute force method), chromosomes with integrated DNA carrying desired genes, proliferation of transformed cells, shoot regeneration, regenerated plant with new trait

Why might the gene gun method of plant transformation be used

Able to transform almost any type of cell and is not limited to transformation of the nucleus. Versatile application

Which 3 crops make up the vast majority of USDA approved genetically modified crops?

Corn, soybean, cotton

What are the most common genetically engineered traits of the 3 most USDA approved GMOs

Herbicide resistance, insect resistance, drought tolerance

What is golden rice? How was the plant modified to achieve this

GM rice to combat vitamin A deficiency. Contains a gene from corn and a gene from bacteria to produce vitamin A

Describe how RNA silencing was used to genetically engineer papaya

Gene from virus integrated into papaya. Viral gene is expressed forming segments of double stranded RNA. The dsRNA triggers the plant’s defense mechanism and are cleaved into short RNA molecules, the short RNA molecules are complementary to the virus. Again, these trigger the plant’s defense mechanism and prevent the virus from replicating

How does CRISPR/Cas9 technology differ from older methods of genetic engineering?

Edit genome without adding foreign DNA

What is an epidemic?

Extensive development of disease in a given geographic area

What are the 5 factors that can lead to the development of an epidemic?

1. Environment favorable for disease development

2. Genetically uniform host population

3. Pathogen 

   1. Endemic, introduced, virulence, genetic diversity

4. Cultural practices favor disease development 

5. Conditions favor vector control

Describe the difference between disease incidence and severity?

Incidence = how many plants are infected

Severity = how much plant tissue is affected

How do spore traps measure the amount of inoculum?

Spore traps measure the amount of spores per cubic meter of air

What is a disease progress curve?

Measurement of disease over time.

What is AUDPC?

Area under the progressive disease curve

Describe a disease progress curve or monocyclic diseases

linear relationship. Slower increase over time. Initial inoculum available is important aspect

Describe a disease progress curve for polycyclic diseases

• Primary inoculum often consists of the sexual spores

• Secondary inoculum are asexual spores

• Exponential growth equation (compound interest)

What is a polyetic disease progress curve? Examples

• Inoculum builds up over seasons

• Regions where there is no break between growing seasons

• Perennial or monocultures over many seasons

How can GIS be used in disease epidemiology

Spatial understanding of how soil conditions and plant health might correlate with  pathogen populations. Yield maps, remote sensing of plant stress. Mapping hot spots of disease presence or biomass

What is seed degeneration? How does it lead to increased disease pressure in the field?

Initial planting of healthy seeds, external inoculum pressure, seed is harvested from plants that may not appear diseased but are, diseased seeds and healthy seeds interplanted, increase of primary inoculum next growing season

Consider the formula for the disease progress curve for polycyclic diseases q = q0e^kt. What are some strategies for reducing t

Planting dates, short term varieties

Consider the formula for the disease progress curve for polycyclic diseases q = q0e^kt. What are some strategies for reducing q0

Vertical resistance, chemical control, sanitaiton

Consider the formula for the disease progress curve for polycyclic diseases q = q0e^kt. What are some strategies for reducing k

Horizontal resistance, protectant chemicals, cultural practices, environment

What is infection period?

Incubation period where a plant is infected but shows no signs or symptoms

How does infection period feed into disease forecasting models?

The accumulation of infection period can be used to create severity values

• Severity values can be used to establish action thresholds for disease management